Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs

Background: It was long assumed that proteins are at least 100 amino acids (AAs) long. Moreover, the detection of short translation products (e. g. coded from small Open Reading Frames, sORFs) is very difficult as the short length makes it hard to distinguish true coding ORFs from ORFs occurring by chance. Nevertheless, over the past few years many such non-canonical genes (with ORFs < 100 AAs) have been discovered in different organisms like Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster. Thanks to advances in sequencing, bioinformatics and computing power, it is now possible to scan the genome in unprecedented scrutiny, for example in a search of this type of small ORFs. Results: Using bioinformatics methods, we performed a systematic search for putatively functional sORFs in the Mus musculus genome. A genome-wide scan detected all sORFs which were subsequently analyzed for their coding potential, based on evolutionary conservation at the AA level, and ranked using a Support Vector Machine (SVM) learning model. The ranked sORFs are finally overlapped with ribosome profiling data, hinting to sORF translation. All candidates are visually inspected using an in-house developed genome browser. In this way dozens of highly conserved sORFs, targeted by ribosomes were identified in the mouse genome, putatively encoding micropeptides. Conclusion: Our combined genome-wide approach leads to the prediction of a comprehensive but manageable set of putatively coding sORFs, a very important first step towards the identification of a new class of bioactive peptides, called micropeptides

Health and longevity studies in C. elegans: the ‘‘healthy worm database’’ reveals strengths, weaknesses and gaps of test compound-based studies

Several biogerontology databases exist that focus on genetic or gene expression data linked to health as well as survival, subsequent to compound treatments or genetic manipulations in animal models. However, none of these has yet collected experimental results of compound-related health changes. Since quality of life is often regarded as more valuable than length of life, we aim to fill this gap with the ‘‘Healthy Worm Database’’ (http://healthy-worm-database.eu). Literature describing health-related compound studies in the aging model Caenorhabditis elegans was screened, and data for 440 compounds collected. The database considers 189 publications describing 89 different phenotypes measured in 2995 different conditions. Besides enabling a targeted search for promising compounds for further investigations, this database also offers insights into the research field of studies on healthy aging based on a frequently used model organism. Some weaknesses of C. elegansbased aging studies, like underrepresented phenotypes, especially concerning cognitive functions, as well as the convenience-based use of young worms as the starting point for compound treatment or phenotype measurement are discussed. In conclusion, the database provides an anchor for the search for compounds affecting health, with a link to public databases, and it further highlights some potential shortcomings in current aging research.Peer Reviewe

Identification of healthspan-promoting genes in Caenorhabditis elegans based on a human GWAS study

To find drivers of healthy ageing, a genome-wide association study (GWAS) was performed in healthy and unhealthy older individuals. Healthy individuals were defined as free from cardiovascular disease, stroke, heart failure, major adverse cardiovascular event, diabetes, dementia, cancer, chronic obstructive pulmonary disease (COPD), asthma, rheumatism, Crohn’s disease, malabsorption or kidney disease. Six single nucleotide polymorphisms (SNPs) with unknown function associated with ten human genes were identified as candidate healthspan markers. Thirteen homologous or closely related genes were selected in the model organism C. elegans for evaluating healthspan after targeted RNAi-mediated knockdown using pathogen resistance, muscle integrity, chemotaxis index and the activity of known longevity and stress response pathways as healthspan reporters. In addition, lifespan was monitored in the RNAi-treated nematodes. RNAi knockdown of yap-1, wwp-1, paxt-1 and several acdh genes resulted in heterogeneous phenotypes regarding muscle integrity, pathogen resistance, chemotactic behaviour, and lifespan. Based on these observations, we hypothesize that their human homologues WWC2, CDKN2AIP and ACADS may play a role in health maintenance in the elderly

V474 Car: A Rare Halo RS CVn Binary in Retrograde Galactic Orbit

We report the discovery that the star V474 Car is an extremely active, high velocity halo RS CVn system. The star was originally identified as a possible pre-main sequence star in Carina, given its enhanced stellar activity, rapid rotation (10.3 days), enhanced Li, and absolute magnitude that places it above the main sequence. However, its extreme radial velocity (264 km s$^{-1}$) suggested that this system was unlike any previously known pre-MS system. Our detailed spectroscopic analysis of echelle spectra taken with the CTIO 4-m finds that V474 Car is both a spectroscopic binary with orbital period similar to the photometric rotation period, and metal poor ([Fe/H] $\simeq -$0.99). The star's Galactic orbit is extremely eccentric (e $\simeq$ 0.93) with perigalacticon of only $\sim$0.3 kpc of the Galactic center - and its eccentricity and smallness of its perigalacticon are only surpassed by $\sim$0.05%, of local F/G-type field stars. The observed characteristics are consistent with V474 Car being a high velocity, metal poor, tidally-locked chromospherically active binary (CAB), i.e.\ a halo RS CVn binary, and one of only a few such specimens known.Comment: Accepted to Astronomical Journa

Crystal structure of Porphyromonas gingivalis dipeptidyl peptidase 4 and structure-activity relationships based on inhibitor profiling

The Gram-negative anaerobe Porphyromonas gingivalis is associated with chronic periodontitis. Clinical isolates of P. gingivalis strains with high dipeptidyl peptidase 4 (DPP4) expression also had a high capacity for biofilm formation and were more infective. The X-ray crystal structure of P. gingivalis DPP4 was solved at 2.2 Å resolution. Despite a sequence identity of 32%, the overall structure of the dimer was conserved between P. gingivalis DPP4 and mammalian orthologues. The structures of the substrate binding sites were also conserved, except for the region called S2-extensive, which is exploited by specific human DPP4 inhibitors currently used as antidiabetic drugs. Screening of a collection of 450 compounds as inhibitors revealed a structure-activity relationship that mimics in part that of mammalian DPP9. The functional similarity between human and bacterial DPP4 was confirmed using 124 potential peptide substrates

The Brown Dwarf Kinematics Project (BDKP) I. Proper Motions and Tangential Velocities for a Large Sample of Late-type M, L and T Dwarfs

We report proper motion measurements for 427 late-type M, L and T dwarfs, 332 of which have been measured for the first time. Combining these new proper motions with previously published measurements yields a sample of 841 M7-T8 dwarfs. We combined parallax measurements or calculated spectrophotometric distances and computed tangential velocities for the entire sample. We find that kinematics for the full and volume-limited 20 pc samples are consistent with those expected for the Galactic thin disk, with no significant differences between late-type M, L, and T dwarfs. Applying an age-velocity relation we conclude that the average kinematic age of the 20 pc sample of ultracool dwarfs is older than recent kinematic estimates and more consistent with age results calculated with population synthesis models. There is a statistically distinct population of high tangential velocity sources whose kinematics suggest an even older population of ultracool dwarfs belonging to either the Galactic thick disk or halo. We isolate subsets of the entire sample, including low surface-gravity dwarfs, unusually blue L dwarfs, and photometric outliers in J-Ks color and investigate their kinematics. We find that the spectroscopically distinct class of unusually blue L dwarfs has kinematics clearly consistent with old age, implying that high surface-gravity and/or low metallicity may be relevant to their spectral properties. The low surface-gravity dwarfs are kinematically younger than the overall population, and the kinematics of the red and blue ultracool dwarfs suggest ages that are younger and older than the full sample, respectively. We also present a reduced proper motion diagram at 2MASS Ks for the entire population and find that a limit of H_Ks > 18 excludes M dwarfs from the L and T dwarf population regardless of near-infrared color.Comment: Accepted for publication in the Astronomical Journal, 21 pages text, 12 tables, 12 figure

The kinematics of late type stars in the solar cylinder studied with SDSS data

We study the velocity distribution of Milky Way disk stars in a kiloparsec-sized region around the Sun, based on ~ 2 million M-type stars from DR7 of SDSS, which have newly re-calibrated absolute proper motions from combining SDSS positions with the USNO-B catalogue. We estimate photometric distances to all stars, accurate to ~ 20 %, and combine them with the proper motions to derive tangential velocities for this kinematically unbiased sample of stars. Based on a statistical de-projection method we then derive the vertical profiles (to heights of Z = 800 pc above the disk plane) for the first and second moments of the three dimensional stellar velocity distribution. We find that = -7 +/- 1 km/s and = -9 +/- 1 km/s, independent of height above the mid-plane, reflecting the Sun's motion with respect to the local standard of rest. In contrast, changes distinctly from -20 +/- 2 km/s in the mid-plane to = -32 km/s at Z = 800 pc, reflecting an asymmetric drift of the stellar mean velocity that increases with height. All three components of the M-star velocity dispersion show a strong linear rise away from the mid-plane, most notably \sigma_{ZZ}, which grows from 18 km/s (Z = 0) to 40 km/s (at Z = 800 pc). We determine the orientation of the velocity ellipsoid, and find a significant vertex deviation of 20 to 25 degrees, which decreases only slightly to heights of Z = 800 pc. Away from the mid-plane, our sample exhibits a remarkably large tilt of the velocity ellipsoid towards the Galactic plane, which reaches 20 deg. at Z = 800 pc and which is not easily explained. Finally, we determine the ratio \sigma^2_{\phi\phi}/\sigma^2_{RR} near the mid-plane, which in the epicyclic approximation implies an almost perfectly flat rotation curve at the Solar radius.Comment: 18 pages, 9 figures, accepted to Astron.